arrayQualityMetrics error
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Paulo Nuin ▴ 200
@paulo-nuin-3012
Last seen 6.9 years ago
Canada
Hi everyone We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. It goes fine until section 5, were it is interrupted by an error > arrayQualityMetrics(rawAffyData, outdir="quality", force=T) The report will be written into directory 'quality'. [[1]] [[2]] [[3]] [[4]] Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" In addition: There were 39 warnings (use warnings() to see them) Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. Cheers Paulo > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 affyPLM_1.26.0 [5] preprocessCore_1.12.0 gcrma_2.22.0 [7] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6
arrayQualityMetrics arrayQualityMetrics • 1.1k views
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@manca-marco-path-4295
Last seen 7.2 years ago
Could it be related to the installation of the library libxml2 on your linux machine? Could you give us your capabilities() and traceback() after the error message? All the best, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Paulo Nuin [nuin at genedrift.org] Inviato: mercoled? 9 febbraio 2011 21.38 A: bioconductor at stat.math.ethz.ch Oggetto: [BioC] arrayQualityMetrics error Hi everyone We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. It goes fine until section 5, were it is interrupted by an error > arrayQualityMetrics(rawAffyData, outdir="quality", force=T) The report will be written into directory 'quality'. [[1]] [[2]] [[3]] [[4]] Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" In addition: There were 39 warnings (use warnings() to see them) Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. Cheers Paulo > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 affyPLM_1.26.0 [5] preprocessCore_1.12.0 gcrma_2.22.0 [7] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Here it is: Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" In addition: There were 38 warnings (use warnings() to see them) > traceback() 18: xmlAttrs(node, addNamespace) 17: xmlGetAttr(clipPath[["path"]], "d") 16: getRect(xmlGetAttr(clipPath[["path"]], "d")) 15: getPlotRegion(n) 14: FUN(X[[1L]], ...) 13: lapply(X, FUN, ...) 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) 11: getPlotRegionNodes(doc) 10: is.vector(X) 9: lapply(getPlotRegionNodes(doc), getPlotPoints) 8: getPlotPoints.XMLInternalDocument(doc) 7: annotationInfo$getfun(doc) 6: aqm.highlight(doc, annotationInfo = annotationInfo) 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg) 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i]) 3: aqm.writereport(reporttitle, expressionset, obj) 2: arrayQualityMetrics(rawAffyData, outdir = "output/quality", force = T) 1: arrayQualityMetrics(rawAffyData, outdir = "output/quality", force = T) > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE BTW, I'm running on CentOS release 5.5 (Final) and libxml2 is libxml2-2.6.26-2.1.2.8.el5_5.1 Thanks Paulo On 2011-02-09, at 4:02 PM, Manca Marco (PATH) wrote: > > Could it be related to the installation of the library libxml2 on your linux machine? > > Could you give us your capabilities() and traceback() after the error message? > > All the best, Marco > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > ******************************************************************** ************************************************* > ________________________________________ > Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Paulo Nuin [nuin at genedrift.org] > Inviato: mercoled? 9 febbraio 2011 21.38 > A: bioconductor at stat.math.ethz.ch > Oggetto: [BioC] arrayQualityMetrics error > > Hi everyone > > We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. > > It goes fine until section 5, were it is interrupted by an error > >> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) > The report will be written into directory 'quality'. > [[1]] > > [[2]] > > [[3]] > > [[4]] > > Error in UseMethod("xmlAttrs", node) : > no applicable method for 'xmlAttrs' applied to an object of class "NULL" > In addition: There were 39 warnings (use warnings() to see them) > > Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. > > Cheers > Paulo > >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp sockets > TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE > libxml fifo cledit iconv NLS profmem cairo > TRUE TRUE TRUE TRUE TRUE FALSE TRUE > > > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 > [3] vsn_3.18.0 affyPLM_1.26.0 > [5] preprocessCore_1.12.0 gcrma_2.22.0 > [7] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 > [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 > [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 > [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 > [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 > [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 > [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 > [25] xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 7.2 years ago
Hi Paulo, On 02/09/2011 09:38 PM, Paulo Nuin wrote: > Hi everyone > > We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. > > It goes fine until section 5, were it is interrupted by an error > >> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) > The report will be written into directory 'quality'. > [[1]] > > [[2]] > > [[3]] > > [[4]] > > Error in UseMethod("xmlAttrs", node) : > no applicable method for 'xmlAttrs' applied to an object of class "NULL" > In addition: There were 39 warnings (use warnings() to see them) The same happened on my system, the problem was a very old version of cairo, see this thread: https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. HTH, James. > > Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. > > Cheers > Paulo > >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp sockets > TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE > libxml fifo cledit iconv NLS profmem cairo > TRUE TRUE TRUE TRUE TRUE FALSE TRUE > > > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 > [3] vsn_3.18.0 affyPLM_1.26.0 > [5] preprocessCore_1.12.0 gcrma_2.22.0 > [7] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 > [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 > [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 > [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 > [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 > [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 > [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 > [25] xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi James I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. Thanks a lot for your help. Paulo On 2011-02-09, at 4:03 PM, James F. Reid wrote: > Hi Paulo, > > > On 02/09/2011 09:38 PM, Paulo Nuin wrote: >> Hi everyone >> >> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >> >> It goes fine until section 5, were it is interrupted by an error >> >>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >> The report will be written into directory 'quality'. >> [[1]] >> >> [[2]] >> >> [[3]] >> >> [[4]] >> >> Error in UseMethod("xmlAttrs", node) : >> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >> In addition: There were 39 warnings (use warnings() to see them) > > The same happened on my system, the problem was a very old version of cairo, see this thread: > https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html > Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. > > HTH, > James. > > > >> >> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >> >> Cheers >> Paulo >> >>> capabilities() >> jpeg png tiff tcltk X11 aqua http/ftp sockets >> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >> libxml fifo cledit iconv NLS profmem cairo >> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >> >> >> >>> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >> [3] vsn_3.18.0 affyPLM_1.26.0 >> [5] preprocessCore_1.12.0 gcrma_2.22.0 >> [7] affy_1.28.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >> [25] xtable_1.5-6 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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Dear Paulo there have been many improvements on the package since the last release, and I would recommend trying the devel version >=3.4.8 http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. The package is in a state of beta-testing, with - the presentation of the outlier detection in the reports not yet fully cooked, - and I am not yet sure whether & how well it works on 64bit Windows. I hope to finalise this within a week or three; any user experiences and comments are welcome. A sneal preview of the new reports is here [2]. Wolfgang [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/20110128/ca068 c82/attachment.pl [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN Paulo Nuin scripsit 10/02/11 02:10: > Hi James > > I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. > > Thanks a lot for your help. > > Paulo > > > On 2011-02-09, at 4:03 PM, James F. Reid wrote: > >> Hi Paulo, >> >> >> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>> Hi everyone >>> >>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>> >>> It goes fine until section 5, were it is interrupted by an error >>> >>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>> The report will be written into directory 'quality'. >>> [[1]] >>> >>> [[2]] >>> >>> [[3]] >>> >>> [[4]] >>> >>> Error in UseMethod("xmlAttrs", node) : >>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> In addition: There were 39 warnings (use warnings() to see them) >> >> The same happened on my system, the problem was a very old version of cairo, see this thread: >> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >> >> HTH, >> James. >> >> >> >>> >>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>> >>> Cheers >>> Paulo >>> >>>> capabilities() >>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>> libxml fifo cledit iconv NLS profmem cairo >>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>> >>> >>> >>>> sessionInfo() >>> R version 2.12.1 (2010-12-16) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>> [3] vsn_3.18.0 affyPLM_1.26.0 >>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>> [7] affy_1.28.0 Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>> [25] xtable_1.5-6 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: > arrayQualityMetrics(rawAffyData, outdir="quality", force=T) The report will be written into directory 'quality'. Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PNG In addition: Warning message: In png(file = nameimg, h = h * dpi, w = w * dpi) : unable to open connection to X11 display '' Here are the capabilities > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got Interfaces supported: X11 External libraries: readline Additional capabilities: PNG, JPEG, TIFF, NLS, cairo Options enabled: shared BLAS, R profiling All X11 (xorg-devel) libraries are installed. Thanks again for the help. Cheers Paulo On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: > Dear Paulo > > there have been many improvements on the package since the last release, and I would recommend trying the devel version >=3.4.8 > > http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html > > which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. > > The package is in a state of beta-testing, with > - the presentation of the outlier detection in the reports not yet fully cooked, > - and I am not yet sure whether & how well it works on 64bit Windows. > > I hope to finalise this within a week or three; any user experiences and comments are welcome. > > A sneal preview of the new reports is here [2]. > > Wolfgang > > > [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/20110128 /ca068c82/attachment.pl > [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN > > > Paulo Nuin scripsit 10/02/11 02:10: >> Hi James >> >> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >> >> Thanks a lot for your help. >> >> Paulo >> >> >> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >> >>> Hi Paulo, >>> >>> >>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>> Hi everyone >>>> >>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>> >>>> It goes fine until section 5, were it is interrupted by an error >>>> >>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>> The report will be written into directory 'quality'. >>>> [[1]] >>>> >>>> [[2]] >>>> >>>> [[3]] >>>> >>>> [[4]] >>>> >>>> Error in UseMethod("xmlAttrs", node) : >>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>> In addition: There were 39 warnings (use warnings() to see them) >>> >>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>> >>> HTH, >>> James. >>> >>> >>> >>>> >>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>> >>>> Cheers >>>> Paulo >>>> >>>>> capabilities() >>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>> libxml fifo cledit iconv NLS profmem cairo >>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>> >>>> >>>> >>>>> sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>> [7] affy_1.28.0 Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>> [25] xtable_1.5-6 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Paulo what happens if you type system("xclock&") (Or, in the Unix shell, simply "xclock&"). Do you see a clock? One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. Why R's png() device needs an X11 server is a different story... Best wishes Wolfgang Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: > Hi Wolfgang > > Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: > >> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) > The report will be written into directory 'quality'. > Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : > unable to start device PNG > In addition: Warning message: > In png(file = nameimg, h = h * dpi, w = w * dpi) : > unable to open connection to X11 display '' > > Here are the capabilities > >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp sockets > TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE > libxml fifo cledit iconv NLS profmem cairo > TRUE TRUE TRUE TRUE TRUE FALSE TRUE > > > Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got > > Interfaces supported: X11 > External libraries: readline > Additional capabilities: PNG, JPEG, TIFF, NLS, cairo > Options enabled: shared BLAS, R profiling > > All X11 (xorg-devel) libraries are installed. > > Thanks again for the help. > > Cheers > Paulo > > > > > On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: > >> Dear Paulo >> >> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >> >> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >> >> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >> >> The package is in a state of beta-testing, with >> - the presentation of the outlier detection in the reports not yet fully cooked, >> - and I am not yet sure whether& how well it works on 64bit Windows. >> >> I hope to finalise this within a week or three; any user experiences and comments are welcome. >> >> A sneal preview of the new reports is here [2]. >> >> Wolfgang >> >> >> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/2011012 8/ca068c82/attachment.pl >> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >> >> >> Paulo Nuin scripsit 10/02/11 02:10: >>> Hi James >>> >>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>> >>> Thanks a lot for your help. >>> >>> Paulo >>> >>> >>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>> >>>> Hi Paulo, >>>> >>>> >>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>> Hi everyone >>>>> >>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>> >>>>> It goes fine until section 5, were it is interrupted by an error >>>>> >>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>> The report will be written into directory 'quality'. >>>>> [[1]] >>>>> >>>>> [[2]] >>>>> >>>>> [[3]] >>>>> >>>>> [[4]] >>>>> >>>>> Error in UseMethod("xmlAttrs", node) : >>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>> In addition: There were 39 warnings (use warnings() to see them) >>>> >>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>> >>>> HTH, >>>> James. >>>> >>>> >>>> >>>>> >>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>> >>>>> Cheers >>>>> Paulo >>>>> >>>>>> capabilities() >>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>> libxml fifo cledit iconv NLS profmem cairo >>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>> >>>>> >>>>> >>>>>> sessionInfo() >>>>> R version 2.12.1 (2010-12-16) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>> [25] xtable_1.5-6 >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine. Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback: > arrayQualityMetrics(rawAffyData, outdir="quality", force=T) The report will be written into directory 'quality'. Error in UseMethod("xmlAttrs", node) : no applicable method for 'xmlAttrs' applied to an object of class "NULL" > traceback() 16: xmlAttrs(node, addNamespace) 15: xmlGetAttr(clipPath[["path"]], "d") 14: getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: lapply(getPlotRegionNodes(doc), getPlotPoints) 6: getPlotPoints.XMLInternalDocument(doc) 5: annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo = module at svg, name = name) 3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, arrayTable = arrayTableCompact, outdir = outdir) 2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, outdir = outdir) 1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T) I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine. Thanks again. If I have any comments or ideas for the package, I let you know. Cheers Paulo On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: > Paulo > > what happens if you type > > system("xclock&") > > (Or, in the Unix shell, simply "xclock&"). Do you see a clock? > > One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. > > Why R's png() device needs an X11 server is a different story... > > Best wishes > Wolfgang > > Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: >> >>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >> The report will be written into directory 'quality'. >> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : >> unable to start device PNG >> In addition: Warning message: >> In png(file = nameimg, h = h * dpi, w = w * dpi) : >> unable to open connection to X11 display '' >> >> Here are the capabilities >> >>> capabilities() >> jpeg png tiff tcltk X11 aqua http/ftp sockets >> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE >> libxml fifo cledit iconv NLS profmem cairo >> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >> >> >> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got >> >> Interfaces supported: X11 >> External libraries: readline >> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >> Options enabled: shared BLAS, R profiling >> >> All X11 (xorg-devel) libraries are installed. >> >> Thanks again for the help. >> >> Cheers >> Paulo >> >> >> >> >> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >> >>> Dear Paulo >>> >>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >>> >>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>> >>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>> >>> The package is in a state of beta-testing, with >>> - the presentation of the outlier detection in the reports not yet fully cooked, >>> - and I am not yet sure whether& how well it works on 64bit Windows. >>> >>> I hope to finalise this within a week or three; any user experiences and comments are welcome. >>> >>> A sneal preview of the new reports is here [2]. >>> >>> Wolfgang >>> >>> >>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/201101 28/ca068c82/attachment.pl >>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>> >>> >>> Paulo Nuin scripsit 10/02/11 02:10: >>>> Hi James >>>> >>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>>> >>>> Thanks a lot for your help. >>>> >>>> Paulo >>>> >>>> >>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>> >>>>> Hi Paulo, >>>>> >>>>> >>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>> Hi everyone >>>>>> >>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>>> >>>>>> It goes fine until section 5, were it is interrupted by an error >>>>>> >>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>> The report will be written into directory 'quality'. >>>>>> [[1]] >>>>>> >>>>>> [[2]] >>>>>> >>>>>> [[3]] >>>>>> >>>>>> [[4]] >>>>>> >>>>>> Error in UseMethod("xmlAttrs", node) : >>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>>> In addition: There were 39 warnings (use warnings() to see them) >>>>> >>>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>> >>>>> HTH, >>>>> James. >>>>> >>>>> >>>>> >>>>>> >>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>>> >>>>>> Cheers >>>>>> Paulo >>>>>> >>>>>>> capabilities() >>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>> >>>>>> >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.12.1 (2010-12-16) >>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>>> [25] xtable_1.5-6 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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Dear Paulo what's your sessionInfo()? Wolfgang Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: > Hi Wolfgang > > Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine. > > Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback: > > >> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) > The report will be written into directory 'quality'. > Error in UseMethod("xmlAttrs", node) : > no applicable method for 'xmlAttrs' applied to an object of class "NULL" >> traceback() > 16: xmlAttrs(node, addNamespace) > 15: xmlGetAttr(clipPath[["path"]], "d") > 14: getRect(xmlGetAttr(clipPath[["path"]], "d")) > 13: getPlotRegion(n) > 12: FUN(X[[1L]], ...) > 11: lapply(X, FUN, ...) > 10: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) > 9: getPlotRegionNodes(doc) > 8: is.vector(X) > 7: lapply(getPlotRegionNodes(doc), getPlotPoints) > 6: getPlotPoints.XMLInternalDocument(doc) > 5: annotationInfo at getPlotObjNodes(doc) > 4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir, > annotationInfo = module at svg, name = name) > 3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, > arrayTable = arrayTableCompact, outdir = outdir) > 2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, > outdir = outdir) > 1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T) > > > I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine. > > Thanks again. If I have any comments or ideas for the package, I let you know. > > Cheers > Paulo > > On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: > >> Paulo >> >> what happens if you type >> >> system("xclock&") >> >> (Or, in the Unix shell, simply "xclock&"). Do you see a clock? >> >> One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. >> >> Why R's png() device needs an X11 server is a different story... >> >> Best wishes >> Wolfgang >> >> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>> Hi Wolfgang >>> >>> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: >>> >>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>> The report will be written into directory 'quality'. >>> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> In png(file = nameimg, h = h * dpi, w = w * dpi) : >>> unable to open connection to X11 display '' >>> >>> Here are the capabilities >>> >>>> capabilities() >>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE >>> libxml fifo cledit iconv NLS profmem cairo >>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>> >>> >>> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got >>> >>> Interfaces supported: X11 >>> External libraries: readline >>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >>> Options enabled: shared BLAS, R profiling >>> >>> All X11 (xorg-devel) libraries are installed. >>> >>> Thanks again for the help. >>> >>> Cheers >>> Paulo >>> >>> >>> >>> >>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>> >>>> Dear Paulo >>>> >>>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >>>> >>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>> >>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>> >>>> The package is in a state of beta-testing, with >>>> - the presentation of the outlier detection in the reports not yet fully cooked, >>>> - and I am not yet sure whether& how well it works on 64bit Windows. >>>> >>>> I hope to finalise this within a week or three; any user experiences and comments are welcome. >>>> >>>> A sneal preview of the new reports is here [2]. >>>> >>>> Wolfgang >>>> >>>> >>>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/20110 128/ca068c82/attachment.pl >>>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>> >>>> >>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>> Hi James >>>>> >>>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>>>> >>>>> Thanks a lot for your help. >>>>> >>>>> Paulo >>>>> >>>>> >>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>> >>>>>> Hi Paulo, >>>>>> >>>>>> >>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>> Hi everyone >>>>>>> >>>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>>>> >>>>>>> It goes fine until section 5, were it is interrupted by an error >>>>>>> >>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>>> The report will be written into directory 'quality'. >>>>>>> [[1]] >>>>>>> >>>>>>> [[2]] >>>>>>> >>>>>>> [[3]] >>>>>>> >>>>>>> [[4]] >>>>>>> >>>>>>> Error in UseMethod("xmlAttrs", node) : >>>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>>>> In addition: There were 39 warnings (use warnings() to see them) >>>>>> >>>>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>> >>>>>> HTH, >>>>>> James. >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>>>> >>>>>>> Cheers >>>>>>> Paulo >>>>>>> >>>>>>>> capabilities() >>>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>>> >>>>>>> >>>>>>> >>>>>>>> sessionInfo() >>>>>>> R version 2.12.1 (2010-12-16) >>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>>>> [25] xtable_1.5-6 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> -- >>>> >>>> >>>> Wolfgang Huber >>>> EMBL >>>> http://www.embl.de/research/units/genome_biology/huber >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang Here's just after running ReadAffy: > sessionInfo() R version 2.13.0 Under development (unstable) (2011-01-30 r54169) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.4.8 affy_1.29.2 [3] Biobase_2.11.8 loaded via a namespace (and not attached): [1] affyio_1.19.4 affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 XML_3.2-0 xtable_1.5-6 after running arrayQualityMetrics the only difference is the addition of hgu133plus2cdf_2.7.0 to the list. Thanks again Paulo On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: > Dear Paulo > > what's your sessionInfo()? > > Wolfgang > > Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine. >> >> Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback: >> >> >>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >> The report will be written into directory 'quality'. >> Error in UseMethod("xmlAttrs", node) : >> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> traceback() >> 16: xmlAttrs(node, addNamespace) >> 15: xmlGetAttr(clipPath[["path"]], "d") >> 14: getRect(xmlGetAttr(clipPath[["path"]], "d")) >> 13: getPlotRegion(n) >> 12: FUN(X[[1L]], ...) >> 11: lapply(X, FUN, ...) >> 10: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >> 9: getPlotRegionNodes(doc) >> 8: is.vector(X) >> 7: lapply(getPlotRegionNodes(doc), getPlotPoints) >> 6: getPlotPoints.XMLInternalDocument(doc) >> 5: annotationInfo at getPlotObjNodes(doc) >> 4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir, >> annotationInfo = module at svg, name = name) >> 3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, >> arrayTable = arrayTableCompact, outdir = outdir) >> 2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, >> outdir = outdir) >> 1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T) >> >> >> I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine. >> >> Thanks again. If I have any comments or ideas for the package, I let you know. >> >> Cheers >> Paulo >> >> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >> >>> Paulo >>> >>> what happens if you type >>> >>> system("xclock&") >>> >>> (Or, in the Unix shell, simply "xclock&"). Do you see a clock? >>> >>> One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. >>> >>> Why R's png() device needs an X11 server is a different story... >>> >>> Best wishes >>> Wolfgang >>> >>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>> Hi Wolfgang >>>> >>>> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: >>>> >>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>> The report will be written into directory 'quality'. >>>> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : >>>> unable to start device PNG >>>> In addition: Warning message: >>>> In png(file = nameimg, h = h * dpi, w = w * dpi) : >>>> unable to open connection to X11 display '' >>>> >>>> Here are the capabilities >>>> >>>>> capabilities() >>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE >>>> libxml fifo cledit iconv NLS profmem cairo >>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>> >>>> >>>> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got >>>> >>>> Interfaces supported: X11 >>>> External libraries: readline >>>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >>>> Options enabled: shared BLAS, R profiling >>>> >>>> All X11 (xorg-devel) libraries are installed. >>>> >>>> Thanks again for the help. >>>> >>>> Cheers >>>> Paulo >>>> >>>> >>>> >>>> >>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>> >>>>> Dear Paulo >>>>> >>>>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >>>>> >>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>> >>>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>> >>>>> The package is in a state of beta-testing, with >>>>> - the presentation of the outlier detection in the reports not yet fully cooked, >>>>> - and I am not yet sure whether& how well it works on 64bit Windows. >>>>> >>>>> I hope to finalise this within a week or three; any user experiences and comments are welcome. >>>>> >>>>> A sneal preview of the new reports is here [2]. >>>>> >>>>> Wolfgang >>>>> >>>>> >>>>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/2011 0128/ca068c82/attachment.pl >>>>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>> >>>>> >>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>> Hi James >>>>>> >>>>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>>>>> >>>>>> Thanks a lot for your help. >>>>>> >>>>>> Paulo >>>>>> >>>>>> >>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>> >>>>>>> Hi Paulo, >>>>>>> >>>>>>> >>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>> Hi everyone >>>>>>>> >>>>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>>>>> >>>>>>>> It goes fine until section 5, were it is interrupted by an error >>>>>>>> >>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>>>> The report will be written into directory 'quality'. >>>>>>>> [[1]] >>>>>>>> >>>>>>>> [[2]] >>>>>>>> >>>>>>>> [[3]] >>>>>>>> >>>>>>>> [[4]] >>>>>>>> >>>>>>>> Error in UseMethod("xmlAttrs", node) : >>>>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>>>>> In addition: There were 39 warnings (use warnings() to see them) >>>>>>> >>>>>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>> >>>>>>> HTH, >>>>>>> James. >>>>>>> >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>>>>> >>>>>>>> Cheers >>>>>>>> Paulo >>>>>>>> >>>>>>>>> capabilities() >>>>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> sessionInfo() >>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>>> >>>>>>>> locale: >>>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>>>>> >>>>>>>> loaded via a namespace (and not attached): >>>>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>>>>> [25] xtable_1.5-6 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor at r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> Wolfgang Huber >>>>> EMBL >>>>> http://www.embl.de/research/units/genome_biology/huber >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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Dear Paulo Can you try with a more recent "Cairo" package (i.e. 1.4-6)? Wolfgang Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: > Hi Wolfgang > > Here's just after running ReadAffy: > >> sessionInfo() > R version 2.13.0 Under development (unstable) (2011-01-30 r54169) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.4.8 affy_1.29.2 > [3] Biobase_2.11.8 > > loaded via a namespace (and not attached): > [1] affyio_1.19.4 affyPLM_1.27.6 annotate_1.29.2 > [4] AnnotationDbi_1.13.13 beadarray_2.1.10 Biostrings_2.19.9 > [7] Cairo_1.4-5 cluster_1.13.2 DBI_0.2-5 > [10] genefilter_1.33.0 grid_2.13.0 Hmisc_3.8-3 > [13] hwriter_1.3 IRanges_1.9.21 lattice_0.19-17 > [16] latticeExtra_0.6-14 limma_3.7.22 marray_1.29.1 > [19] preprocessCore_1.13.5 RColorBrewer_1.0-2 RJSONIO_0.4-1 > [22] RSQLite_0.9-4 setRNG_2009.11-1 splines_2.13.0 > [25] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.13.0 > [28] vsn_3.19.3 XML_3.2-0 xtable_1.5-6 > > after running arrayQualityMetrics the only difference is the addition of hgu133plus2cdf_2.7.0 to the list. > > Thanks again > > Paulo > > > > > > > On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: > >> Dear Paulo >> >> what's your sessionInfo()? >> >> Wolfgang >> >> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>> Hi Wolfgang >>> >>> Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine. >>> >>> Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback: >>> >>> >>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>> The report will be written into directory 'quality'. >>> Error in UseMethod("xmlAttrs", node) : >>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>> traceback() >>> 16: xmlAttrs(node, addNamespace) >>> 15: xmlGetAttr(clipPath[["path"]], "d") >>> 14: getRect(xmlGetAttr(clipPath[["path"]], "d")) >>> 13: getPlotRegion(n) >>> 12: FUN(X[[1L]], ...) >>> 11: lapply(X, FUN, ...) >>> 10: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >>> 9: getPlotRegionNodes(doc) >>> 8: is.vector(X) >>> 7: lapply(getPlotRegionNodes(doc), getPlotPoints) >>> 6: getPlotPoints.XMLInternalDocument(doc) >>> 5: annotationInfo at getPlotObjNodes(doc) >>> 4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir, >>> annotationInfo = module at svg, name = name) >>> 3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, >>> arrayTable = arrayTableCompact, outdir = outdir) >>> 2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, >>> outdir = outdir) >>> 1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T) >>> >>> >>> I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine. >>> >>> Thanks again. If I have any comments or ideas for the package, I let you know. >>> >>> Cheers >>> Paulo >>> >>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>> >>>> Paulo >>>> >>>> what happens if you type >>>> >>>> system("xclock&") >>>> >>>> (Or, in the Unix shell, simply "xclock&"). Do you see a clock? >>>> >>>> One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. >>>> >>>> Why R's png() device needs an X11 server is a different story... >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>> Hi Wolfgang >>>>> >>>>> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: >>>>> >>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>> The report will be written into directory 'quality'. >>>>> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : >>>>> unable to start device PNG >>>>> In addition: Warning message: >>>>> In png(file = nameimg, h = h * dpi, w = w * dpi) : >>>>> unable to open connection to X11 display '' >>>>> >>>>> Here are the capabilities >>>>> >>>>>> capabilities() >>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE >>>>> libxml fifo cledit iconv NLS profmem cairo >>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>> >>>>> >>>>> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got >>>>> >>>>> Interfaces supported: X11 >>>>> External libraries: readline >>>>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >>>>> Options enabled: shared BLAS, R profiling >>>>> >>>>> All X11 (xorg-devel) libraries are installed. >>>>> >>>>> Thanks again for the help. >>>>> >>>>> Cheers >>>>> Paulo >>>>> >>>>> >>>>> >>>>> >>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>> >>>>>> Dear Paulo >>>>>> >>>>>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >>>>>> >>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>> >>>>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>> >>>>>> The package is in a state of beta-testing, with >>>>>> - the presentation of the outlier detection in the reports not yet fully cooked, >>>>>> - and I am not yet sure whether& how well it works on 64bit Windows. >>>>>> >>>>>> I hope to finalise this within a week or three; any user experiences and comments are welcome. >>>>>> >>>>>> A sneal preview of the new reports is here [2]. >>>>>> >>>>>> Wolfgang >>>>>> >>>>>> >>>>>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/201 10128/ca068c82/attachment.pl >>>>>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>> >>>>>> >>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>> Hi James >>>>>>> >>>>>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>>>>>> >>>>>>> Thanks a lot for your help. >>>>>>> >>>>>>> Paulo >>>>>>> >>>>>>> >>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>> >>>>>>>> Hi Paulo, >>>>>>>> >>>>>>>> >>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>> Hi everyone >>>>>>>>> >>>>>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>>>>>> >>>>>>>>> It goes fine until section 5, were it is interrupted by an error >>>>>>>>> >>>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>>>>> The report will be written into directory 'quality'. >>>>>>>>> [[1]] >>>>>>>>> >>>>>>>>> [[2]] >>>>>>>>> >>>>>>>>> [[3]] >>>>>>>>> >>>>>>>>> [[4]] >>>>>>>>> >>>>>>>>> Error in UseMethod("xmlAttrs", node) : >>>>>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>>>>>> In addition: There were 39 warnings (use warnings() to see them) >>>>>>>> >>>>>>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>> >>>>>>>> HTH, >>>>>>>> James. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Paulo >>>>>>>>> >>>>>>>>>> capabilities() >>>>>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> sessionInfo() >>>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>>>> >>>>>>>>> locale: >>>>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>>>> >>>>>>>>> attached base packages: >>>>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>>>> >>>>>>>>> other attached packages: >>>>>>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>>>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>>>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>>>>>> >>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>>>>>> [25] xtable_1.5-6 >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioconductor mailing list >>>>>>>>> Bioconductor at r-project.org >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> >>>>>> Wolfgang Huber >>>>>> EMBL >>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> -- >>>> >>>> >>>> Wolfgang Huber >>>> EMBL >>>> http://www.embl.de/research/units/genome_biology/huber >>>> >>>> >>> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang I'm not able to install a newer version on my CentOS. The only official package for Cairo is 1.2.4. I didn't find a way to compile R and point it to a locally compiled Cairo (in /opt) and I don't know if it's possible to manage the compilation of packages in order to use this Cairo compile too. Thanks Paulo On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: > Dear Paulo > > Can you try with a more recent "Cairo" package (i.e. 1.4-6)? > > Wolfgang > > Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> Here's just after running ReadAffy: >> >>> sessionInfo() >> R version 2.13.0 Under development (unstable) (2011-01-30 r54169) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] arrayQualityMetrics_3.4.8 affy_1.29.2 >> [3] Biobase_2.11.8 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.19.4 affyPLM_1.27.6 annotate_1.29.2 >> [4] AnnotationDbi_1.13.13 beadarray_2.1.10 Biostrings_2.19.9 >> [7] Cairo_1.4-5 cluster_1.13.2 DBI_0.2-5 >> [10] genefilter_1.33.0 grid_2.13.0 Hmisc_3.8-3 >> [13] hwriter_1.3 IRanges_1.9.21 lattice_0.19-17 >> [16] latticeExtra_0.6-14 limma_3.7.22 marray_1.29.1 >> [19] preprocessCore_1.13.5 RColorBrewer_1.0-2 RJSONIO_0.4-1 >> [22] RSQLite_0.9-4 setRNG_2009.11-1 splines_2.13.0 >> [25] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.13.0 >> [28] vsn_3.19.3 XML_3.2-0 xtable_1.5-6 >> >> after running arrayQualityMetrics the only difference is the addition of hgu133plus2cdf_2.7.0 to the list. >> >> Thanks again >> >> Paulo >> >> >> >> >> >> >> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >> >>> Dear Paulo >>> >>> what's your sessionInfo()? >>> >>> Wolfgang >>> >>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>> Hi Wolfgang >>>> >>>> Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine. >>>> >>>> Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback: >>>> >>>> >>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>> The report will be written into directory 'quality'. >>>> Error in UseMethod("xmlAttrs", node) : >>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>> traceback() >>>> 16: xmlAttrs(node, addNamespace) >>>> 15: xmlGetAttr(clipPath[["path"]], "d") >>>> 14: getRect(xmlGetAttr(clipPath[["path"]], "d")) >>>> 13: getPlotRegion(n) >>>> 12: FUN(X[[1L]], ...) >>>> 11: lapply(X, FUN, ...) >>>> 10: sapply(tmp, function(n) all(getPlotRegion(n) == vb)) >>>> 9: getPlotRegionNodes(doc) >>>> 8: is.vector(X) >>>> 7: lapply(getPlotRegionNodes(doc), getPlotPoints) >>>> 6: getPlotPoints.XMLInternalDocument(doc) >>>> 5: annotationInfo at getPlotObjNodes(doc) >>>> 4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir, >>>> annotationInfo = module at svg, name = name) >>>> 3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, >>>> arrayTable = arrayTableCompact, outdir = outdir) >>>> 2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, >>>> outdir = outdir) >>>> 1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T) >>>> >>>> >>>> I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine. >>>> >>>> Thanks again. If I have any comments or ideas for the package, I let you know. >>>> >>>> Cheers >>>> Paulo >>>> >>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>> >>>>> Paulo >>>>> >>>>> what happens if you type >>>>> >>>>> system("xclock&") >>>>> >>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a clock? >>>>> >>>>> One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding. >>>>> >>>>> Why R's png() device needs an X11 server is a different story... >>>>> >>>>> Best wishes >>>>> Wolfgang >>>>> >>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>> Hi Wolfgang >>>>>> >>>>>> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again: >>>>>> >>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>> The report will be written into directory 'quality'. >>>>>> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : >>>>>> unable to start device PNG >>>>>> In addition: Warning message: >>>>>> In png(file = nameimg, h = h * dpi, w = w * dpi) : >>>>>> unable to open connection to X11 display '' >>>>>> >>>>>> Here are the capabilities >>>>>> >>>>>>> capabilities() >>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE >>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>> >>>>>> >>>>>> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got >>>>>> >>>>>> Interfaces supported: X11 >>>>>> External libraries: readline >>>>>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >>>>>> Options enabled: shared BLAS, R profiling >>>>>> >>>>>> All X11 (xorg-devel) libraries are installed. >>>>>> >>>>>> Thanks again for the help. >>>>>> >>>>>> Cheers >>>>>> Paulo >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>> >>>>>>> Dear Paulo >>>>>>> >>>>>>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8 >>>>>>> >>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>> >>>>>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>> >>>>>>> The package is in a state of beta-testing, with >>>>>>> - the presentation of the outlier detection in the reports not yet fully cooked, >>>>>>> - and I am not yet sure whether& how well it works on 64bit Windows. >>>>>>> >>>>>>> I hope to finalise this within a week or three; any user experiences and comments are welcome. >>>>>>> >>>>>>> A sneal preview of the new reports is here [2]. >>>>>>> >>>>>>> Wolfgang >>>>>>> >>>>>>> >>>>>>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/20 110128/ca068c82/attachment.pl >>>>>>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>> >>>>>>> >>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>> Hi James >>>>>>>> >>>>>>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list. >>>>>>>> >>>>>>>> Thanks a lot for your help. >>>>>>>> >>>>>>>> Paulo >>>>>>>> >>>>>>>> >>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>> >>>>>>>>> Hi Paulo, >>>>>>>>> >>>>>>>>> >>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>> Hi everyone >>>>>>>>>> >>>>>>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. >>>>>>>>>> >>>>>>>>>> It goes fine until section 5, were it is interrupted by an error >>>>>>>>>> >>>>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T) >>>>>>>>>> The report will be written into directory 'quality'. >>>>>>>>>> [[1]] >>>>>>>>>> >>>>>>>>>> [[2]] >>>>>>>>>> >>>>>>>>>> [[3]] >>>>>>>>>> >>>>>>>>>> [[4]] >>>>>>>>>> >>>>>>>>>> Error in UseMethod("xmlAttrs", node) : >>>>>>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>>>>>>>>> In addition: There were 39 warnings (use warnings() to see them) >>>>>>>>> >>>>>>>>> The same happened on my system, the problem was a very old version of cairo, see this thread: >>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> James. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated. >>>>>>>>>> >>>>>>>>>> Cheers >>>>>>>>>> Paulo >>>>>>>>>> >>>>>>>>>>> capabilities() >>>>>>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets >>>>>>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE >>>>>>>>>> libxml fifo cledit iconv NLS profmem cairo >>>>>>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> sessionInfo() >>>>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>>>>> >>>>>>>>>> other attached packages: >>>>>>>>>> [1] hgu133plus2cdf_2.7.0 arrayQualityMetrics_3.2.4 >>>>>>>>>> [3] vsn_3.18.0 affyPLM_1.26.0 >>>>>>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0 >>>>>>>>>> [7] affy_1.28.0 Biobase_2.10.0 >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>>>>>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5 >>>>>>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3 >>>>>>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13 >>>>>>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>>>>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 >>>>>>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2 >>>>>>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0 >>>>>>>>>> [25] xtable_1.5-6 >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list >>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor at r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> >>>>>>> Wolfgang Huber >>>>>>> EMBL >>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> Wolfgang Huber >>>>> EMBL >>>>> http://www.embl.de/research/units/genome_biology/huber >>>>> >>>>> >>>> >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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Paulo perhaps you are trying to make things more complicated than necessary. What happens when you enter source("http://www.bioconductor.org/biocLite.R") biocLite("Cairo") into your R command line? I am not sure what you mean by 'official package', the package page on CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 1.4-6. I noted though that older versions are sticking around on the internet. Also note that the "Cairo" R package is not the same as the "cairo graphics library" e.g. at http://www.cairographics.org. You should not need to put anything into /opt or point R to it or anything like that. Best wishes Wolfgang Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto: > Hi Wolfgang > > I'm not able to install a newer version on my CentOS. The only > official package for Cairo is 1.2.4. I didn't find a way to compile R > and point it to a locally compiled Cairo (in /opt) and I don't know > if it's possible to manage the compilation of packages in order to > use this Cairo compile too. > > Thanks > > Paulo > > > > On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: > >> Dear Paulo >> >> Can you try with a more recent "Cairo" package (i.e. 1.4-6)? >> >> Wolfgang >> >> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >>> Hi Wolfgang >>> >>> Here's just after running ReadAffy: >>> >>>> sessionInfo() >>> R version 2.13.0 Under development (unstable) (2011-01-30 >>> r54169) Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] >>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >>> LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] >>> LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C >>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>> LC_IDENTIFICATION=C >>> >>> attached base packages: [1] stats graphics grDevices utils >>> datasets methods base >>> >>> other attached packages: [1] arrayQualityMetrics_3.4.8 >>> affy_1.29.2 [3] Biobase_2.11.8 >>> >>> loaded via a namespace (and not attached): [1] affyio_1.19.4 >>> affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 >>> beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 >>> cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 >>> grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 >>> IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 >>> limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 >>> RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 >>> setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 >>> SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 >>> XML_3.2-0 xtable_1.5-6 >>> >>> after running arrayQualityMetrics the only difference is the >>> addition of hgu133plus2cdf_2.7.0 to the list. >>> >>> Thanks again >>> >>> Paulo >>> >>> >>> >>> >>> >>> >>> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >>> >>>> Dear Paulo >>>> >>>> what's your sessionInfo()? >>>> >>>> Wolfgang >>>> >>>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>>> Hi Wolfgang >>>>> >>>>> Indeed, if I create an X11 tunnel, everything turns ok on the >>>>> X11 side. My mistake, as the system is remote and some of the >>>>> tests we run on a local machine. >>>>> >>>>> Nonetheless, we still find a problem at the end of the run, >>>>> and it's similar to what we experienced the first time. Here >>>>> is the error and traceback: >>>>> >>>>> >>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>> force=T) >>>>> The report will be written into directory 'quality'. Error in >>>>> UseMethod("xmlAttrs", node) : no applicable method for >>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>> traceback() >>>>> 16: xmlAttrs(node, addNamespace) 15: >>>>> xmlGetAttr(clipPath[["path"]], "d") 14: >>>>> getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: >>>>> getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, >>>>> ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == >>>>> vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: >>>>> lapply(getPlotRegionNodes(doc), getPlotPoints) 6: >>>>> getPlotPoints.XMLInternalDocument(doc) 5: >>>>> annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile >>>>> = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo >>>>> = module at svg, name = name) 3: reportModule(p = p, module = >>>>> modules[[i]], currentIndex = currentIndex, arrayTable = >>>>> arrayTableCompact, outdir = outdir) 2: >>>>> aqm.writereport(modules = m, arrayTable = x$pData, >>>>> reporttitle = reporttitle, outdir = outdir) 1: >>>>> arrayQualityMetrics(rawAffyData, outdir = "quality", force = >>>>> T) >>>>> >>>>> >>>>> I guess this is still related to Cairo's version. I will >>>>> probably try to use another version of Linux in another >>>>> machine. >>>>> >>>>> Thanks again. If I have any comments or ideas for the >>>>> package, I let you know. >>>>> >>>>> Cheers Paulo >>>>> >>>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>>> >>>>>> Paulo >>>>>> >>>>>> what happens if you type >>>>>> >>>>>> system("xclock&") >>>>>> >>>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a >>>>>> clock? >>>>>> >>>>>> One possible explanation, if you are logging into a server >>>>>> remotely, that you have not enable X11 forwarding. >>>>>> >>>>>> Why R's png() device needs an X11 server is a different >>>>>> story... >>>>>> >>>>>> Best wishes Wolfgang >>>>>> >>>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>>> Hi Wolfgang >>>>>>> >>>>>>> Thanks a lot for your message. I was able to install this >>>>>>> version, both on a release version and on a devel version >>>>>>> of R, but I'm running into an error again: >>>>>>> >>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>> force=T) >>>>>>> The report will be written into directory 'quality'. >>>>>>> Error in X11(paste("png::", filename, sep = ""), width, >>>>>>> height, pointsize, : unable to start device PNG In >>>>>>> addition: Warning message: In png(file = nameimg, h = h * >>>>>>> dpi, w = w * dpi) : unable to open connection to X11 >>>>>>> display '' >>>>>>> >>>>>>> Here are the capabilities >>>>>>> >>>>>>>> capabilities() >>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>> FALSE FALSE TRUE TRUE libxml fifo cledit >>>>>>> iconv NLS profmem cairo TRUE TRUE TRUE >>>>>>> TRUE TRUE FALSE TRUE >>>>>>> >>>>>>> >>>>>>> Both versions are the same. I don't know if the error is >>>>>>> due to X11 being FALSE. I don't understand why X11 is >>>>>>> showing as FALSE, as the binaries were compiled with the >>>>>>> --with-x flag, and at the end of configure we got >>>>>>> >>>>>>> Interfaces supported: X11 External libraries: >>>>>>> readline Additional capabilities: PNG, JPEG, TIFF, NLS, >>>>>>> cairo Options enabled: shared BLAS, R >>>>>>> profiling >>>>>>> >>>>>>> All X11 (xorg-devel) libraries are installed. >>>>>>> >>>>>>> Thanks again for the help. >>>>>>> >>>>>>> Cheers Paulo >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>>> >>>>>>>> Dear Paulo >>>>>>>> >>>>>>>> there have been many improvements on the package since >>>>>>>> the last release, and I would recommend trying the >>>>>>>> devel version>=3.4.8 >>>>>>>> >>>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>>> >>>>>>>> >>>>>>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>>> >>>>>>>> The package is in a state of beta-testing, with - the >>>>>>>> presentation of the outlier detection in the reports >>>>>>>> not yet fully cooked, - and I am not yet sure whether& >>>>>>>> how well it works on 64bit Windows. >>>>>>>> >>>>>>>> I hope to finalise this within a week or three; any >>>>>>>> user experiences and comments are welcome. >>>>>>>> >>>>>>>> A sneal preview of the new reports is here [2]. >>>>>>>> >>>>>>>> Wolfgang >>>>>>>> >>>>>>>> >>>>>>>> [1] >>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/attachments/20110 128/ca068c82/attachment.pl >>>>>>>> >>>>>>>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>>> >>>>>>>> >>>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>>> Hi James >>>>>>>>> >>>>>>>>> I checked our Cairo version, and it seems quite old. >>>>>>>>> I'm checking the best way to update, as we are using >>>>>>>>> CentOS official package. If the problem persists >>>>>>>>> after upgrade, I will report to the list. >>>>>>>>> >>>>>>>>> Thanks a lot for your help. >>>>>>>>> >>>>>>>>> Paulo >>>>>>>>> >>>>>>>>> >>>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>>> >>>>>>>>>> Hi Paulo, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>>> Hi everyone >>>>>>>>>>> >>>>>>>>>>> We just got a new HPC system to speed up our >>>>>>>>>>> analysis, but we are having some problems with >>>>>>>>>>> the end part of a arrayQualityMetrics run. >>>>>>>>>>> >>>>>>>>>>> It goes fine until section 5, were it is >>>>>>>>>>> interrupted by an error >>>>>>>>>>> >>>>>>>>>>>> arrayQualityMetrics(rawAffyData, >>>>>>>>>>>> outdir="quality", force=T) >>>>>>>>>>> The report will be written into directory >>>>>>>>>>> 'quality'. [[1]] >>>>>>>>>>> >>>>>>>>>>> [[2]] >>>>>>>>>>> >>>>>>>>>>> [[3]] >>>>>>>>>>> >>>>>>>>>>> [[4]] >>>>>>>>>>> >>>>>>>>>>> Error in UseMethod("xmlAttrs", node) : no >>>>>>>>>>> applicable method for 'xmlAttrs' applied to an >>>>>>>>>>> object of class "NULL" In addition: There were 39 >>>>>>>>>>> warnings (use warnings() to see them) >>>>>>>>>> >>>>>>>>>> The same happened on my system, the problem was a >>>>>>>>>> very old version of cairo, see this thread: >>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>>> >>>>>>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>>> >>>>>>>>>> HTH, James. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Our sessionInfo and capabilities are below. R is >>>>>>>>>>> compiled natively and most of the required >>>>>>>>>>> libraries are present and compiled with the >>>>>>>>>>> system. Any help is appreciated. >>>>>>>>>>> >>>>>>>>>>> Cheers Paulo >>>>>>>>>>> >>>>>>>>>>>> capabilities() >>>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>>> TRUE FALSE TRUE TRUE libxml fifo >>>>>>>>>>> cledit iconv NLS profmem cairo TRUE >>>>>>>>>>> TRUE TRUE TRUE TRUE FALSE >>>>>>>>>>> TRUE >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> sessionInfo() >>>>>>>>>>> R version 2.12.1 (2010-12-16) Platform: >>>>>>>>>>> x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>>> >>>>>>>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 >>>>>>>>>>> LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 >>>>>>>>>>> LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C >>>>>>>>>>> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 >>>>>>>>>>> LC_NAME=C [9] LC_ADDRESS=C >>>>>>>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>>>>>>> LC_IDENTIFICATION=C >>>>>>>>>>> >>>>>>>>>>> attached base packages: [1] stats graphics >>>>>>>>>>> grDevices utils datasets methods base >>>>>>>>>>> >>>>>>>>>>> other attached packages: [1] hgu133plus2cdf_2.7.0 >>>>>>>>>>> arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 >>>>>>>>>>> affyPLM_1.26.0 [5] preprocessCore_1.12.0 >>>>>>>>>>> gcrma_2.22.0 [7] affy_1.28.0 >>>>>>>>>>> Biobase_2.10.0 >>>>>>>>>>> >>>>>>>>>>> loaded via a namespace (and not attached): [1] >>>>>>>>>>> affyio_1.18.0 annotate_1.28.0 >>>>>>>>>>> AnnotationDbi_1.12.0 [4] beadarray_2.0.3 >>>>>>>>>>> Biostrings_2.18.2 DBI_0.2-5 [7] >>>>>>>>>>> genefilter_1.32.0 grid_2.12.1 >>>>>>>>>>> hwriter_1.3 [10] IRanges_1.8.8 >>>>>>>>>>> KernSmooth_2.23-4 lattice_0.19-13 [13] >>>>>>>>>>> latticeExtra_0.6-14 limma_3.6.9 >>>>>>>>>>> marray_1.28.0 [16] RColorBrewer_1.0-2 >>>>>>>>>>> RSQLite_0.9-4 simpleaffy_2.26.1 [19] >>>>>>>>>>> splines_2.12.1 stats4_2.12.1 >>>>>>>>>>> survival_2.36-2 [22] SVGAnnotation_0.7-2 >>>>>>>>>>> tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>> >>>>>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>> Search the archives: >>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> -- >>>>>>>> >>>>>>>> >>>>>>>> Wolfgang Huber EMBL >>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: >>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>> >>>>>> >>>>>>>> -- >>>>>> >>>>>> >>>>>> Wolfgang Huber EMBL >>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>> >>>>>> >>>>> >>>> >>>> -- >>>> >>>> >>>> Wolfgang Huber EMBL >>>> http://www.embl.de/research/units/genome_biology/huber >>>> >>>> >>> >> >> -- >> >> >> Wolfgang Huber EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang I know what you mean. If I try to install Cairo (the BioC package) it compiles fine, but it still relies on the cairographics that it's installed in the system: > biocLite("Cairo") ... checking for configurable backends... cairo cairo-ft cairo-pdf cairo- png cairo-ps cairo-xlib cairo-xlib-xrender configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12 ? gcc -std=gnu99 -shared -L/usr/local/lib64 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf- backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lfontconfig -lpng12 -lz -lXrender -lcairo -lX11 -ljpeg -ltiff installing to /home/nuin/R/x86_64-unknown-linux-gnu- library/2.13/Cairo/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (Cairo) CentOS "official" cairographics is 1.2.4, which is quite old. I'm not able to install a newer cairographics in /usr or I can break my system. I can compile another newer version of cairographics on /opt, but them I would have to make the BioC's Cairo to point to /opt include and library dirs. Thanks again Paulo On 2011-02-13, at 6:22 AM, Wolfgang Huber wrote: > Paulo > > perhaps you are trying to make things more complicated than necessary. > What happens when you enter > > source("http://www.bioconductor.org/biocLite.R") > biocLite("Cairo") > > into your R command line? > > I am not sure what you mean by 'official package', the package page on CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 1.4-6. I noted though that older versions are sticking around on the internet. Also note that the "Cairo" R package is not the same as the "cairo graphics library" e.g. at http://www.cairographics.org. You should not need to put anything into /opt or point R to it or anything like that. > > Best wishes > Wolfgang > > > > > > > Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> I'm not able to install a newer version on my CentOS. The only >> official package for Cairo is 1.2.4. I didn't find a way to compile R >> and point it to a locally compiled Cairo (in /opt) and I don't know >> if it's possible to manage the compilation of packages in order to >> use this Cairo compile too. >> >> Thanks >> >> Paulo >> >> >> >> On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: >> >>> Dear Paulo >>> >>> Can you try with a more recent "Cairo" package (i.e. 1.4-6)? >>> >>> Wolfgang >>> >>> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >>>> Hi Wolfgang >>>> >>>> Here's just after running ReadAffy: >>>> >>>>> sessionInfo() >>>> R version 2.13.0 Under development (unstable) (2011-01-30 >>>> r54169) Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] >>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >>>> LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] >>>> LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C >>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>> LC_IDENTIFICATION=C >>>> >>>> attached base packages: [1] stats graphics grDevices utils >>>> datasets methods base >>>> >>>> other attached packages: [1] arrayQualityMetrics_3.4.8 >>>> affy_1.29.2 [3] Biobase_2.11.8 >>>> >>>> loaded via a namespace (and not attached): [1] affyio_1.19.4 >>>> affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 >>>> beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 >>>> cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 >>>> grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 >>>> IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 >>>> limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 >>>> RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 >>>> setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 >>>> SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 >>>> XML_3.2-0 xtable_1.5-6 >>>> >>>> after running arrayQualityMetrics the only difference is the >>>> addition of hgu133plus2cdf_2.7.0 to the list. >>>> >>>> Thanks again >>>> >>>> Paulo >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >>>> >>>>> Dear Paulo >>>>> >>>>> what's your sessionInfo()? >>>>> >>>>> Wolfgang >>>>> >>>>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>>>> Hi Wolfgang >>>>>> >>>>>> Indeed, if I create an X11 tunnel, everything turns ok on the >>>>>> X11 side. My mistake, as the system is remote and some of the >>>>>> tests we run on a local machine. >>>>>> >>>>>> Nonetheless, we still find a problem at the end of the run, >>>>>> and it's similar to what we experienced the first time. Here >>>>>> is the error and traceback: >>>>>> >>>>>> >>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>> force=T) >>>>>> The report will be written into directory 'quality'. Error in >>>>>> UseMethod("xmlAttrs", node) : no applicable method for >>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>> traceback() >>>>>> 16: xmlAttrs(node, addNamespace) 15: >>>>>> xmlGetAttr(clipPath[["path"]], "d") 14: >>>>>> getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: >>>>>> getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, >>>>>> ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == >>>>>> vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: >>>>>> lapply(getPlotRegionNodes(doc), getPlotPoints) 6: >>>>>> getPlotPoints.XMLInternalDocument(doc) 5: >>>>>> annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile >>>>>> = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo >>>>>> = module at svg, name = name) 3: reportModule(p = p, module = >>>>>> modules[[i]], currentIndex = currentIndex, arrayTable = >>>>>> arrayTableCompact, outdir = outdir) 2: >>>>>> aqm.writereport(modules = m, arrayTable = x$pData, >>>>>> reporttitle = reporttitle, outdir = outdir) 1: >>>>>> arrayQualityMetrics(rawAffyData, outdir = "quality", force = >>>>>> T) >>>>>> >>>>>> >>>>>> I guess this is still related to Cairo's version. I will >>>>>> probably try to use another version of Linux in another >>>>>> machine. >>>>>> >>>>>> Thanks again. If I have any comments or ideas for the >>>>>> package, I let you know. >>>>>> >>>>>> Cheers Paulo >>>>>> >>>>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>>>> >>>>>>> Paulo >>>>>>> >>>>>>> what happens if you type >>>>>>> >>>>>>> system("xclock&") >>>>>>> >>>>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a >>>>>>> clock? >>>>>>> >>>>>>> One possible explanation, if you are logging into a server >>>>>>> remotely, that you have not enable X11 forwarding. >>>>>>> >>>>>>> Why R's png() device needs an X11 server is a different >>>>>>> story... >>>>>>> >>>>>>> Best wishes Wolfgang >>>>>>> >>>>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>>>> Hi Wolfgang >>>>>>>> >>>>>>>> Thanks a lot for your message. I was able to install this >>>>>>>> version, both on a release version and on a devel version >>>>>>>> of R, but I'm running into an error again: >>>>>>>> >>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>> force=T) >>>>>>>> The report will be written into directory 'quality'. >>>>>>>> Error in X11(paste("png::", filename, sep = ""), width, >>>>>>>> height, pointsize, : unable to start device PNG In >>>>>>>> addition: Warning message: In png(file = nameimg, h = h * >>>>>>>> dpi, w = w * dpi) : unable to open connection to X11 >>>>>>>> display '' >>>>>>>> >>>>>>>> Here are the capabilities >>>>>>>> >>>>>>>>> capabilities() >>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>> FALSE FALSE TRUE TRUE libxml fifo cledit >>>>>>>> iconv NLS profmem cairo TRUE TRUE TRUE >>>>>>>> TRUE TRUE FALSE TRUE >>>>>>>> >>>>>>>> >>>>>>>> Both versions are the same. I don't know if the error is >>>>>>>> due to X11 being FALSE. I don't understand why X11 is >>>>>>>> showing as FALSE, as the binaries were compiled with the >>>>>>>> --with-x flag, and at the end of configure we got >>>>>>>> >>>>>>>> Interfaces supported: X11 External libraries: >>>>>>>> readline Additional capabilities: PNG, JPEG, TIFF, NLS, >>>>>>>> cairo Options enabled: shared BLAS, R >>>>>>>> profiling >>>>>>>> >>>>>>>> All X11 (xorg-devel) libraries are installed. >>>>>>>> >>>>>>>> Thanks again for the help. >>>>>>>> >>>>>>>> Cheers Paulo >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>>>> >>>>>>>>> Dear Paulo >>>>>>>>> >>>>>>>>> there have been many improvements on the package since >>>>>>>>> the last release, and I would recommend trying the >>>>>>>>> devel version>=3.4.8 >>>>>>>>> >>>>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>>>> >>>>>>>>> >>>>>>>>> > which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>>>> >>>>>>>>> The package is in a state of beta-testing, with - the >>>>>>>>> presentation of the outlier detection in the reports >>>>>>>>> not yet fully cooked, - and I am not yet sure whether& >>>>>>>>> how well it works on 64bit Windows. >>>>>>>>> >>>>>>>>> I hope to finalise this within a week or three; any >>>>>>>>> user experiences and comments are welcome. >>>>>>>>> >>>>>>>>> A sneal preview of the new reports is here [2]. >>>>>>>>> >>>>>>>>> Wolfgang >>>>>>>>> >>>>>>>>> >>>>>>>>> [1] >>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/attachments/2011 0128/ca068c82/attachment.pl >>>>>>>>> >>>>>>>>> > [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>>>> >>>>>>>>> >>>>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>>>> Hi James >>>>>>>>>> >>>>>>>>>> I checked our Cairo version, and it seems quite old. >>>>>>>>>> I'm checking the best way to update, as we are using >>>>>>>>>> CentOS official package. If the problem persists >>>>>>>>>> after upgrade, I will report to the list. >>>>>>>>>> >>>>>>>>>> Thanks a lot for your help. >>>>>>>>>> >>>>>>>>>> Paulo >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>>>> >>>>>>>>>>> Hi Paulo, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>>>> Hi everyone >>>>>>>>>>>> >>>>>>>>>>>> We just got a new HPC system to speed up our >>>>>>>>>>>> analysis, but we are having some problems with >>>>>>>>>>>> the end part of a arrayQualityMetrics run. >>>>>>>>>>>> >>>>>>>>>>>> It goes fine until section 5, were it is >>>>>>>>>>>> interrupted by an error >>>>>>>>>>>> >>>>>>>>>>>>> arrayQualityMetrics(rawAffyData, >>>>>>>>>>>>> outdir="quality", force=T) >>>>>>>>>>>> The report will be written into directory >>>>>>>>>>>> 'quality'. [[1]] >>>>>>>>>>>> >>>>>>>>>>>> [[2]] >>>>>>>>>>>> >>>>>>>>>>>> [[3]] >>>>>>>>>>>> >>>>>>>>>>>> [[4]] >>>>>>>>>>>> >>>>>>>>>>>> Error in UseMethod("xmlAttrs", node) : no >>>>>>>>>>>> applicable method for 'xmlAttrs' applied to an >>>>>>>>>>>> object of class "NULL" In addition: There were 39 >>>>>>>>>>>> warnings (use warnings() to see them) >>>>>>>>>>> >>>>>>>>>>> The same happened on my system, the problem was a >>>>>>>>>>> very old version of cairo, see this thread: >>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>>>> >>>>>>>>>>> > Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>>>> >>>>>>>>>>> HTH, James. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Our sessionInfo and capabilities are below. R is >>>>>>>>>>>> compiled natively and most of the required >>>>>>>>>>>> libraries are present and compiled with the >>>>>>>>>>>> system. Any help is appreciated. >>>>>>>>>>>> >>>>>>>>>>>> Cheers Paulo >>>>>>>>>>>> >>>>>>>>>>>>> capabilities() >>>>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>>>> TRUE FALSE TRUE TRUE libxml fifo >>>>>>>>>>>> cledit iconv NLS profmem cairo TRUE >>>>>>>>>>>> TRUE TRUE TRUE TRUE FALSE >>>>>>>>>>>> TRUE >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> sessionInfo() >>>>>>>>>>>> R version 2.12.1 (2010-12-16) Platform: >>>>>>>>>>>> x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>>>> >>>>>>>>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 >>>>>>>>>>>> LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 >>>>>>>>>>>> LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C >>>>>>>>>>>> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 >>>>>>>>>>>> LC_NAME=C [9] LC_ADDRESS=C >>>>>>>>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>>>>>>>> LC_IDENTIFICATION=C >>>>>>>>>>>> >>>>>>>>>>>> attached base packages: [1] stats graphics >>>>>>>>>>>> grDevices utils datasets methods base >>>>>>>>>>>> >>>>>>>>>>>> other attached packages: [1] hgu133plus2cdf_2.7.0 >>>>>>>>>>>> arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 >>>>>>>>>>>> affyPLM_1.26.0 [5] preprocessCore_1.12.0 >>>>>>>>>>>> gcrma_2.22.0 [7] affy_1.28.0 >>>>>>>>>>>> Biobase_2.10.0 >>>>>>>>>>>> >>>>>>>>>>>> loaded via a namespace (and not attached): [1] >>>>>>>>>>>> affyio_1.18.0 annotate_1.28.0 >>>>>>>>>>>> AnnotationDbi_1.12.0 [4] beadarray_2.0.3 >>>>>>>>>>>> Biostrings_2.18.2 DBI_0.2-5 [7] >>>>>>>>>>>> genefilter_1.32.0 grid_2.12.1 >>>>>>>>>>>> hwriter_1.3 [10] IRanges_1.8.8 >>>>>>>>>>>> KernSmooth_2.23-4 lattice_0.19-13 [13] >>>>>>>>>>>> latticeExtra_0.6-14 limma_3.6.9 >>>>>>>>>>>> marray_1.28.0 [16] RColorBrewer_1.0-2 >>>>>>>>>>>> RSQLite_0.9-4 simpleaffy_2.26.1 [19] >>>>>>>>>>>> splines_2.12.1 stats4_2.12.1 >>>>>>>>>>>> survival_2.36-2 [22] SVGAnnotation_0.7-2 >>>>>>>>>>>> tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>>> >>>>>>>>>>>> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> Search the archives: >>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> > -- >>>>>>>>> >>>>>>>>> >>>>>>>>> Wolfgang Huber EMBL >>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>> Search the archives: >>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>> >>>>>>> >>>>>>> >>>>>>>>> > -- >>>>>>> >>>>>>> >>>>>>> Wolfgang Huber EMBL >>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> Wolfgang Huber EMBL >>>>> http://www.embl.de/research/units/genome_biology/huber >>>>> >>>>> >>>> >>> >>> -- >>> >>> >>> Wolfgang Huber EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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Dear Paulo sorry - that was my mistake. You were right to ask that question. I had overlooked that the source version of the Cairo R package *does* of course look for cairo libraries on your system. I don't have a CentOS system to test this, but assuming that you use bash, have you tried something like: env CAIRO_CFLAGS="-D_REENTRANT -I/opt/local/include/cairo -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng14" CAIRO_LIBS="-L/opt/local/lib -lfreetype -lpng14 -lz -lXrender -lcairo -lX11" R CMD INSTALL Downloads/Cairo_1.4-6.tar.gz This is all in one line, and the values between the "..." apply to my (Mac OS X with Mac ports) system, you'd need to replace the paths and library names with those applicable on your CentOS. Sorry that this is so painful... Wolfgang Il Feb/13/11 7:36 PM, Paulo Nuin ha scritto: > Hi Wolfgang > > I know what you mean. If I try to install Cairo (the BioC package) it compiles fine, but it still relies on the cairographics that it's installed in the system: > >> biocLite("Cairo") > ... > checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender > configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12 > ? > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf- backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lfontconfig -lpng12 -lz -lXrender -lcairo -lX11 -ljpeg -ltiff > installing to /home/nuin/R/x86_64-unknown-linux-gnu- library/2.13/Cairo/libs > ** R > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > > * DONE (Cairo) > > CentOS "official" cairographics is 1.2.4, which is quite old. I'm not able to install a newer cairographics in /usr or I can break my system. I can compile another newer version of cairographics on /opt, but them I would have to make the BioC's Cairo to point to /opt include and library dirs. > > Thanks again > > Paulo > > > > On 2011-02-13, at 6:22 AM, Wolfgang Huber wrote: > >> Paulo >> >> perhaps you are trying to make things more complicated than necessary. >> What happens when you enter >> >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("Cairo") >> >> into your R command line? >> >> I am not sure what you mean by 'official package', the package page on CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 1.4-6. I noted though that older versions are sticking around on the internet. Also note that the "Cairo" R package is not the same as the "cairo graphics library" e.g. at http://www.cairographics.org. You should not need to put anything into /opt or point R to it or anything like that. >> >> Best wishes >> Wolfgang >> >> >> >> >> >> >> Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto: >>> Hi Wolfgang >>> >>> I'm not able to install a newer version on my CentOS. The only >>> official package for Cairo is 1.2.4. I didn't find a way to compile R >>> and point it to a locally compiled Cairo (in /opt) and I don't know >>> if it's possible to manage the compilation of packages in order to >>> use this Cairo compile too. >>> >>> Thanks >>> >>> Paulo >>> >>> >>> >>> On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: >>> >>>> Dear Paulo >>>> >>>> Can you try with a more recent "Cairo" package (i.e. 1.4-6)? >>>> >>>> Wolfgang >>>> >>>> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >>>>> Hi Wolfgang >>>>> >>>>> Here's just after running ReadAffy: >>>>> >>>>>> sessionInfo() >>>>> R version 2.13.0 Under development (unstable) (2011-01-30 >>>>> r54169) Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] >>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >>>>> LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] >>>>> LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C >>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>> LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: [1] stats graphics grDevices utils >>>>> datasets methods base >>>>> >>>>> other attached packages: [1] arrayQualityMetrics_3.4.8 >>>>> affy_1.29.2 [3] Biobase_2.11.8 >>>>> >>>>> loaded via a namespace (and not attached): [1] affyio_1.19.4 >>>>> affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 >>>>> beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 >>>>> cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 >>>>> grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 >>>>> IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 >>>>> limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 >>>>> RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 >>>>> setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 >>>>> SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 >>>>> XML_3.2-0 xtable_1.5-6 >>>>> >>>>> after running arrayQualityMetrics the only difference is the >>>>> addition of hgu133plus2cdf_2.7.0 to the list. >>>>> >>>>> Thanks again >>>>> >>>>> Paulo >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >>>>> >>>>>> Dear Paulo >>>>>> >>>>>> what's your sessionInfo()? >>>>>> >>>>>> Wolfgang >>>>>> >>>>>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>>>>> Hi Wolfgang >>>>>>> >>>>>>> Indeed, if I create an X11 tunnel, everything turns ok on the >>>>>>> X11 side. My mistake, as the system is remote and some of the >>>>>>> tests we run on a local machine. >>>>>>> >>>>>>> Nonetheless, we still find a problem at the end of the run, >>>>>>> and it's similar to what we experienced the first time. Here >>>>>>> is the error and traceback: >>>>>>> >>>>>>> >>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>> force=T) >>>>>>> The report will be written into directory 'quality'. Error in >>>>>>> UseMethod("xmlAttrs", node) : no applicable method for >>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>>> traceback() >>>>>>> 16: xmlAttrs(node, addNamespace) 15: >>>>>>> xmlGetAttr(clipPath[["path"]], "d") 14: >>>>>>> getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: >>>>>>> getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, >>>>>>> ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == >>>>>>> vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: >>>>>>> lapply(getPlotRegionNodes(doc), getPlotPoints) 6: >>>>>>> getPlotPoints.XMLInternalDocument(doc) 5: >>>>>>> annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile >>>>>>> = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo >>>>>>> = module at svg, name = name) 3: reportModule(p = p, module = >>>>>>> modules[[i]], currentIndex = currentIndex, arrayTable = >>>>>>> arrayTableCompact, outdir = outdir) 2: >>>>>>> aqm.writereport(modules = m, arrayTable = x$pData, >>>>>>> reporttitle = reporttitle, outdir = outdir) 1: >>>>>>> arrayQualityMetrics(rawAffyData, outdir = "quality", force = >>>>>>> T) >>>>>>> >>>>>>> >>>>>>> I guess this is still related to Cairo's version. I will >>>>>>> probably try to use another version of Linux in another >>>>>>> machine. >>>>>>> >>>>>>> Thanks again. If I have any comments or ideas for the >>>>>>> package, I let you know. >>>>>>> >>>>>>> Cheers Paulo >>>>>>> >>>>>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>>>>> >>>>>>>> Paulo >>>>>>>> >>>>>>>> what happens if you type >>>>>>>> >>>>>>>> system("xclock&") >>>>>>>> >>>>>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a >>>>>>>> clock? >>>>>>>> >>>>>>>> One possible explanation, if you are logging into a server >>>>>>>> remotely, that you have not enable X11 forwarding. >>>>>>>> >>>>>>>> Why R's png() device needs an X11 server is a different >>>>>>>> story... >>>>>>>> >>>>>>>> Best wishes Wolfgang >>>>>>>> >>>>>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>>>>> Hi Wolfgang >>>>>>>>> >>>>>>>>> Thanks a lot for your message. I was able to install this >>>>>>>>> version, both on a release version and on a devel version >>>>>>>>> of R, but I'm running into an error again: >>>>>>>>> >>>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>>> force=T) >>>>>>>>> The report will be written into directory 'quality'. >>>>>>>>> Error in X11(paste("png::", filename, sep = ""), width, >>>>>>>>> height, pointsize, : unable to start device PNG In >>>>>>>>> addition: Warning message: In png(file = nameimg, h = h * >>>>>>>>> dpi, w = w * dpi) : unable to open connection to X11 >>>>>>>>> display '' >>>>>>>>> >>>>>>>>> Here are the capabilities >>>>>>>>> >>>>>>>>>> capabilities() >>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>> FALSE FALSE TRUE TRUE libxml fifo cledit >>>>>>>>> iconv NLS profmem cairo TRUE TRUE TRUE >>>>>>>>> TRUE TRUE FALSE TRUE >>>>>>>>> >>>>>>>>> >>>>>>>>> Both versions are the same. I don't know if the error is >>>>>>>>> due to X11 being FALSE. I don't understand why X11 is >>>>>>>>> showing as FALSE, as the binaries were compiled with the >>>>>>>>> --with-x flag, and at the end of configure we got >>>>>>>>> >>>>>>>>> Interfaces supported: X11 External libraries: >>>>>>>>> readline Additional capabilities: PNG, JPEG, TIFF, NLS, >>>>>>>>> cairo Options enabled: shared BLAS, R >>>>>>>>> profiling >>>>>>>>> >>>>>>>>> All X11 (xorg-devel) libraries are installed. >>>>>>>>> >>>>>>>>> Thanks again for the help. >>>>>>>>> >>>>>>>>> Cheers Paulo >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>>>>> >>>>>>>>>> Dear Paulo >>>>>>>>>> >>>>>>>>>> there have been many improvements on the package since >>>>>>>>>> the last release, and I would recommend trying the >>>>>>>>>> devel version>=3.4.8 >>>>>>>>>> >>>>>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>>>>> >>>>>>>>>> The package is in a state of beta-testing, with - the >>>>>>>>>> presentation of the outlier detection in the reports >>>>>>>>>> not yet fully cooked, - and I am not yet sure whether& >>>>>>>>>> how well it works on 64bit Windows. >>>>>>>>>> >>>>>>>>>> I hope to finalise this within a week or three; any >>>>>>>>>> user experiences and comments are welcome. >>>>>>>>>> >>>>>>>>>> A sneal preview of the new reports is here [2]. >>>>>>>>>> >>>>>>>>>> Wolfgang >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> [1] >>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/attachments/201 10128/ca068c82/attachment.pl >>>>>>>>>> >>>>>>>>>> >> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>>>>> Hi James >>>>>>>>>>> >>>>>>>>>>> I checked our Cairo version, and it seems quite old. >>>>>>>>>>> I'm checking the best way to update, as we are using >>>>>>>>>>> CentOS official package. If the problem persists >>>>>>>>>>> after upgrade, I will report to the list. >>>>>>>>>>> >>>>>>>>>>> Thanks a lot for your help. >>>>>>>>>>> >>>>>>>>>>> Paulo >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Paulo, >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>>>>> Hi everyone >>>>>>>>>>>>> >>>>>>>>>>>>> We just got a new HPC system to speed up our >>>>>>>>>>>>> analysis, but we are having some problems with >>>>>>>>>>>>> the end part of a arrayQualityMetrics run. >>>>>>>>>>>>> >>>>>>>>>>>>> It goes fine until section 5, were it is >>>>>>>>>>>>> interrupted by an error >>>>>>>>>>>>> >>>>>>>>>>>>>> arrayQualityMetrics(rawAffyData, >>>>>>>>>>>>>> outdir="quality", force=T) >>>>>>>>>>>>> The report will be written into directory >>>>>>>>>>>>> 'quality'. [[1]] >>>>>>>>>>>>> >>>>>>>>>>>>> [[2]] >>>>>>>>>>>>> >>>>>>>>>>>>> [[3]] >>>>>>>>>>>>> >>>>>>>>>>>>> [[4]] >>>>>>>>>>>>> >>>>>>>>>>>>> Error in UseMethod("xmlAttrs", node) : no >>>>>>>>>>>>> applicable method for 'xmlAttrs' applied to an >>>>>>>>>>>>> object of class "NULL" In addition: There were 39 >>>>>>>>>>>>> warnings (use warnings() to see them) >>>>>>>>>>>> >>>>>>>>>>>> The same happened on my system, the problem was a >>>>>>>>>>>> very old version of cairo, see this thread: >>>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>>>>> >>>>>>>>>>>> >> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>>>>> >>>>>>>>>>>> HTH, James. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Our sessionInfo and capabilities are below. R is >>>>>>>>>>>>> compiled natively and most of the required >>>>>>>>>>>>> libraries are present and compiled with the >>>>>>>>>>>>> system. Any help is appreciated. >>>>>>>>>>>>> >>>>>>>>>>>>> Cheers Paulo >>>>>>>>>>>>> >>>>>>>>>>>>>> capabilities() >>>>>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>>>>> TRUE FALSE TRUE TRUE libxml fifo >>>>>>>>>>>>> cledit iconv NLS profmem cairo TRUE >>>>>>>>>>>>> TRUE TRUE TRUE TRUE FALSE >>>>>>>>>>>>> TRUE >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> sessionInfo() >>>>>>>>>>>>> R version 2.12.1 (2010-12-16) Platform: >>>>>>>>>>>>> x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>>>>> >>>>>>>>>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 >>>>>>>>>>>>> LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 >>>>>>>>>>>>> LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C >>>>>>>>>>>>> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 >>>>>>>>>>>>> LC_NAME=C [9] LC_ADDRESS=C >>>>>>>>>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>>>>>>>>> LC_IDENTIFICATION=C >>>>>>>>>>>>> >>>>>>>>>>>>> attached base packages: [1] stats graphics >>>>>>>>>>>>> grDevices utils datasets methods base >>>>>>>>>>>>> >>>>>>>>>>>>> other attached packages: [1] hgu133plus2cdf_2.7.0 >>>>>>>>>>>>> arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 >>>>>>>>>>>>> affyPLM_1.26.0 [5] preprocessCore_1.12.0 >>>>>>>>>>>>> gcrma_2.22.0 [7] affy_1.28.0 >>>>>>>>>>>>> Biobase_2.10.0 >>>>>>>>>>>>> >>>>>>>>>>>>> loaded via a namespace (and not attached): [1] >>>>>>>>>>>>> affyio_1.18.0 annotate_1.28.0 >>>>>>>>>>>>> AnnotationDbi_1.12.0 [4] beadarray_2.0.3 >>>>>>>>>>>>> Biostrings_2.18.2 DBI_0.2-5 [7] >>>>>>>>>>>>> genefilter_1.32.0 grid_2.12.1 >>>>>>>>>>>>> hwriter_1.3 [10] IRanges_1.8.8 >>>>>>>>>>>>> KernSmooth_2.23-4 lattice_0.19-13 [13] >>>>>>>>>>>>> latticeExtra_0.6-14 limma_3.6.9 >>>>>>>>>>>>> marray_1.28.0 [16] RColorBrewer_1.0-2 >>>>>>>>>>>>> RSQLite_0.9-4 simpleaffy_2.26.1 [19] >>>>>>>>>>>>> splines_2.12.1 stats4_2.12.1 >>>>>>>>>>>>> survival_2.36-2 [22] SVGAnnotation_0.7-2 >>>>>>>>>>>>> tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>>>> >>>>>>>>>>>>> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>> Search the archives: >>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >> -- >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Wolfgang Huber EMBL >>>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> Search the archives: >>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>> >> -- >>>>>>>> >>>>>>>> >>>>>>>> Wolfgang Huber EMBL >>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> >>>>>> Wolfgang Huber EMBL >>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>> >>>>>> >>>>> >>>> >>>> -- >>>> >>>> >>>> Wolfgang Huber EMBL >>>> http://www.embl.de/research/units/genome_biology/huber >>>> >>>> >>> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Hi Wolfgang Thanks again. I tried, but I still get an error saying that Cairo cannot generate an executable (or something in that line). I compiled all libraries manually. I contacted our HPC provided and they will set me up with a newer distro of OpenSUSE so I can use this one instead. Thanks a lot for all the help. I keep you posted if I find any problems or have any comments on the package, which looks great BTW. Cheers Paulo On 2011-02-13, at 5:46 PM, Wolfgang Huber wrote: > Dear Paulo > > sorry - that was my mistake. You were right to ask that question. I had overlooked that the source version of the Cairo R package *does* of course look for cairo libraries on your system. > > I don't have a CentOS system to test this, but assuming that you use bash, have you tried something like: > > env CAIRO_CFLAGS="-D_REENTRANT -I/opt/local/include/cairo -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng14" CAIRO_LIBS="-L/opt/local/lib -lfreetype -lpng14 -lz -lXrender -lcairo -lX11" R CMD INSTALL Downloads/Cairo_1.4-6.tar.gz > > This is all in one line, and the values between the "..." apply to my (Mac OS X with Mac ports) system, you'd need to replace the paths and library names with those applicable on your CentOS. > > Sorry that this is so painful... > > Wolfgang > > > Il Feb/13/11 7:36 PM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> I know what you mean. If I try to install Cairo (the BioC package) it compiles fine, but it still relies on the cairographics that it's installed in the system: >> >>> biocLite("Cairo") >> ... >> checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender >> configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12 >> ? >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf- backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lfontconfig -lpng12 -lz -lXrender -lcairo -lX11 -ljpeg -ltiff >> installing to /home/nuin/R/x86_64-unknown-linux-gnu- library/2.13/Cairo/libs >> ** R >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices ... >> ** testing if installed package can be loaded >> >> * DONE (Cairo) >> >> CentOS "official" cairographics is 1.2.4, which is quite old. I'm not able to install a newer cairographics in /usr or I can break my system. I can compile another newer version of cairographics on /opt, but them I would have to make the BioC's Cairo to point to /opt include and library dirs. >> >> Thanks again >> >> Paulo >> >> >> >> On 2011-02-13, at 6:22 AM, Wolfgang Huber wrote: >> >>> Paulo >>> >>> perhaps you are trying to make things more complicated than necessary. >>> What happens when you enter >>> >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("Cairo") >>> >>> into your R command line? >>> >>> I am not sure what you mean by 'official package', the package page on CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 1.4-6. I noted though that older versions are sticking around on the internet. Also note that the "Cairo" R package is not the same as the "cairo graphics library" e.g. at http://www.cairographics.org. You should not need to put anything into /opt or point R to it or anything like that. >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> >>> >>> >>> Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto: >>>> Hi Wolfgang >>>> >>>> I'm not able to install a newer version on my CentOS. The only >>>> official package for Cairo is 1.2.4. I didn't find a way to compile R >>>> and point it to a locally compiled Cairo (in /opt) and I don't know >>>> if it's possible to manage the compilation of packages in order to >>>> use this Cairo compile too. >>>> >>>> Thanks >>>> >>>> Paulo >>>> >>>> >>>> >>>> On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: >>>> >>>>> Dear Paulo >>>>> >>>>> Can you try with a more recent "Cairo" package (i.e. 1.4-6)? >>>>> >>>>> Wolfgang >>>>> >>>>> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >>>>>> Hi Wolfgang >>>>>> >>>>>> Here's just after running ReadAffy: >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.13.0 Under development (unstable) (2011-01-30 >>>>>> r54169) Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] >>>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >>>>>> LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] >>>>>> LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C >>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>> LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: [1] stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: [1] arrayQualityMetrics_3.4.8 >>>>>> affy_1.29.2 [3] Biobase_2.11.8 >>>>>> >>>>>> loaded via a namespace (and not attached): [1] affyio_1.19.4 >>>>>> affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 >>>>>> beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 >>>>>> cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 >>>>>> grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 >>>>>> IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 >>>>>> limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 >>>>>> RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 >>>>>> setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 >>>>>> SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 >>>>>> XML_3.2-0 xtable_1.5-6 >>>>>> >>>>>> after running arrayQualityMetrics the only difference is the >>>>>> addition of hgu133plus2cdf_2.7.0 to the list. >>>>>> >>>>>> Thanks again >>>>>> >>>>>> Paulo >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >>>>>> >>>>>>> Dear Paulo >>>>>>> >>>>>>> what's your sessionInfo()? >>>>>>> >>>>>>> Wolfgang >>>>>>> >>>>>>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>>>>>> Hi Wolfgang >>>>>>>> >>>>>>>> Indeed, if I create an X11 tunnel, everything turns ok on the >>>>>>>> X11 side. My mistake, as the system is remote and some of the >>>>>>>> tests we run on a local machine. >>>>>>>> >>>>>>>> Nonetheless, we still find a problem at the end of the run, >>>>>>>> and it's similar to what we experienced the first time. Here >>>>>>>> is the error and traceback: >>>>>>>> >>>>>>>> >>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>> force=T) >>>>>>>> The report will be written into directory 'quality'. Error in >>>>>>>> UseMethod("xmlAttrs", node) : no applicable method for >>>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>>>> traceback() >>>>>>>> 16: xmlAttrs(node, addNamespace) 15: >>>>>>>> xmlGetAttr(clipPath[["path"]], "d") 14: >>>>>>>> getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: >>>>>>>> getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, >>>>>>>> ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == >>>>>>>> vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: >>>>>>>> lapply(getPlotRegionNodes(doc), getPlotPoints) 6: >>>>>>>> getPlotPoints.XMLInternalDocument(doc) 5: >>>>>>>> annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile >>>>>>>> = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo >>>>>>>> = module at svg, name = name) 3: reportModule(p = p, module = >>>>>>>> modules[[i]], currentIndex = currentIndex, arrayTable = >>>>>>>> arrayTableCompact, outdir = outdir) 2: >>>>>>>> aqm.writereport(modules = m, arrayTable = x$pData, >>>>>>>> reporttitle = reporttitle, outdir = outdir) 1: >>>>>>>> arrayQualityMetrics(rawAffyData, outdir = "quality", force = >>>>>>>> T) >>>>>>>> >>>>>>>> >>>>>>>> I guess this is still related to Cairo's version. I will >>>>>>>> probably try to use another version of Linux in another >>>>>>>> machine. >>>>>>>> >>>>>>>> Thanks again. If I have any comments or ideas for the >>>>>>>> package, I let you know. >>>>>>>> >>>>>>>> Cheers Paulo >>>>>>>> >>>>>>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>>>>>> >>>>>>>>> Paulo >>>>>>>>> >>>>>>>>> what happens if you type >>>>>>>>> >>>>>>>>> system("xclock&") >>>>>>>>> >>>>>>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a >>>>>>>>> clock? >>>>>>>>> >>>>>>>>> One possible explanation, if you are logging into a server >>>>>>>>> remotely, that you have not enable X11 forwarding. >>>>>>>>> >>>>>>>>> Why R's png() device needs an X11 server is a different >>>>>>>>> story... >>>>>>>>> >>>>>>>>> Best wishes Wolfgang >>>>>>>>> >>>>>>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>>>>>> Hi Wolfgang >>>>>>>>>> >>>>>>>>>> Thanks a lot for your message. I was able to install this >>>>>>>>>> version, both on a release version and on a devel version >>>>>>>>>> of R, but I'm running into an error again: >>>>>>>>>> >>>>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>>>> force=T) >>>>>>>>>> The report will be written into directory 'quality'. >>>>>>>>>> Error in X11(paste("png::", filename, sep = ""), width, >>>>>>>>>> height, pointsize, : unable to start device PNG In >>>>>>>>>> addition: Warning message: In png(file = nameimg, h = h * >>>>>>>>>> dpi, w = w * dpi) : unable to open connection to X11 >>>>>>>>>> display '' >>>>>>>>>> >>>>>>>>>> Here are the capabilities >>>>>>>>>> >>>>>>>>>>> capabilities() >>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>> FALSE FALSE TRUE TRUE libxml fifo cledit >>>>>>>>>> iconv NLS profmem cairo TRUE TRUE TRUE >>>>>>>>>> TRUE TRUE FALSE TRUE >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Both versions are the same. I don't know if the error is >>>>>>>>>> due to X11 being FALSE. I don't understand why X11 is >>>>>>>>>> showing as FALSE, as the binaries were compiled with the >>>>>>>>>> --with-x flag, and at the end of configure we got >>>>>>>>>> >>>>>>>>>> Interfaces supported: X11 External libraries: >>>>>>>>>> readline Additional capabilities: PNG, JPEG, TIFF, NLS, >>>>>>>>>> cairo Options enabled: shared BLAS, R >>>>>>>>>> profiling >>>>>>>>>> >>>>>>>>>> All X11 (xorg-devel) libraries are installed. >>>>>>>>>> >>>>>>>>>> Thanks again for the help. >>>>>>>>>> >>>>>>>>>> Cheers Paulo >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>>>>>> >>>>>>>>>>> Dear Paulo >>>>>>>>>>> >>>>>>>>>>> there have been many improvements on the package since >>>>>>>>>>> the last release, and I would recommend trying the >>>>>>>>>>> devel version>=3.4.8 >>>>>>>>>>> >>>>>>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>>>>>> >>>>>>>>>>> The package is in a state of beta-testing, with - the >>>>>>>>>>> presentation of the outlier detection in the reports >>>>>>>>>>> not yet fully cooked, - and I am not yet sure whether& >>>>>>>>>>> how well it works on 64bit Windows. >>>>>>>>>>> >>>>>>>>>>> I hope to finalise this within a week or three; any >>>>>>>>>>> user experiences and comments are welcome. >>>>>>>>>>> >>>>>>>>>>> A sneal preview of the new reports is here [2]. >>>>>>>>>>> >>>>>>>>>>> Wolfgang >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> [1] >>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/attachments/20 110128/ca068c82/attachment.pl >>>>>>>>>>> >>>>>>>>>>> >>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>>>>>> Hi James >>>>>>>>>>>> >>>>>>>>>>>> I checked our Cairo version, and it seems quite old. >>>>>>>>>>>> I'm checking the best way to update, as we are using >>>>>>>>>>>> CentOS official package. If the problem persists >>>>>>>>>>>> after upgrade, I will report to the list. >>>>>>>>>>>> >>>>>>>>>>>> Thanks a lot for your help. >>>>>>>>>>>> >>>>>>>>>>>> Paulo >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Paulo, >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>>>>>> Hi everyone >>>>>>>>>>>>>> >>>>>>>>>>>>>> We just got a new HPC system to speed up our >>>>>>>>>>>>>> analysis, but we are having some problems with >>>>>>>>>>>>>> the end part of a arrayQualityMetrics run. >>>>>>>>>>>>>> >>>>>>>>>>>>>> It goes fine until section 5, were it is >>>>>>>>>>>>>> interrupted by an error >>>>>>>>>>>>>> >>>>>>>>>>>>>>> arrayQualityMetrics(rawAffyData, >>>>>>>>>>>>>>> outdir="quality", force=T) >>>>>>>>>>>>>> The report will be written into directory >>>>>>>>>>>>>> 'quality'. [[1]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[2]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[3]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[4]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> Error in UseMethod("xmlAttrs", node) : no >>>>>>>>>>>>>> applicable method for 'xmlAttrs' applied to an >>>>>>>>>>>>>> object of class "NULL" In addition: There were 39 >>>>>>>>>>>>>> warnings (use warnings() to see them) >>>>>>>>>>>>> >>>>>>>>>>>>> The same happened on my system, the problem was a >>>>>>>>>>>>> very old version of cairo, see this thread: >>>>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>>>>>> >>>>>>>>>>>>> >>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>>>>>> >>>>>>>>>>>>> HTH, James. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Our sessionInfo and capabilities are below. R is >>>>>>>>>>>>>> compiled natively and most of the required >>>>>>>>>>>>>> libraries are present and compiled with the >>>>>>>>>>>>>> system. Any help is appreciated. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Cheers Paulo >>>>>>>>>>>>>> >>>>>>>>>>>>>>> capabilities() >>>>>>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>>>>>> TRUE FALSE TRUE TRUE libxml fifo >>>>>>>>>>>>>> cledit iconv NLS profmem cairo TRUE >>>>>>>>>>>>>> TRUE TRUE TRUE TRUE FALSE >>>>>>>>>>>>>> TRUE >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> sessionInfo() >>>>>>>>>>>>>> R version 2.12.1 (2010-12-16) Platform: >>>>>>>>>>>>>> x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>>>>>> >>>>>>>>>>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 >>>>>>>>>>>>>> LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 >>>>>>>>>>>>>> LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C >>>>>>>>>>>>>> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 >>>>>>>>>>>>>> LC_NAME=C [9] LC_ADDRESS=C >>>>>>>>>>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>>>>>>>>>> LC_IDENTIFICATION=C >>>>>>>>>>>>>> >>>>>>>>>>>>>> attached base packages: [1] stats graphics >>>>>>>>>>>>>> grDevices utils datasets methods base >>>>>>>>>>>>>> >>>>>>>>>>>>>> other attached packages: [1] hgu133plus2cdf_2.7.0 >>>>>>>>>>>>>> arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 >>>>>>>>>>>>>> affyPLM_1.26.0 [5] preprocessCore_1.12.0 >>>>>>>>>>>>>> gcrma_2.22.0 [7] affy_1.28.0 >>>>>>>>>>>>>> Biobase_2.10.0 >>>>>>>>>>>>>> >>>>>>>>>>>>>> loaded via a namespace (and not attached): [1] >>>>>>>>>>>>>> affyio_1.18.0 annotate_1.28.0 >>>>>>>>>>>>>> AnnotationDbi_1.12.0 [4] beadarray_2.0.3 >>>>>>>>>>>>>> Biostrings_2.18.2 DBI_0.2-5 [7] >>>>>>>>>>>>>> genefilter_1.32.0 grid_2.12.1 >>>>>>>>>>>>>> hwriter_1.3 [10] IRanges_1.8.8 >>>>>>>>>>>>>> KernSmooth_2.23-4 lattice_0.19-13 [13] >>>>>>>>>>>>>> latticeExtra_0.6-14 limma_3.6.9 >>>>>>>>>>>>>> marray_1.28.0 [16] RColorBrewer_1.0-2 >>>>>>>>>>>>>> RSQLite_0.9-4 simpleaffy_2.26.1 [19] >>>>>>>>>>>>>> splines_2.12.1 stats4_2.12.1 >>>>>>>>>>>>>> survival_2.36-2 [22] SVGAnnotation_0.7-2 >>>>>>>>>>>>>> tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>>> Search the archives: >>>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>> -- >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Wolfgang Huber EMBL >>>>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioconductor mailing list Bioconductor at r-project.org >>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>> Search the archives: >>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>>> >>> -- >>>>>>>>> >>>>>>>>> >>>>>>>>> Wolfgang Huber EMBL >>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> >>>>>>> Wolfgang Huber EMBL >>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> Wolfgang Huber EMBL >>>>> http://www.embl.de/research/units/genome_biology/huber >>>>> >>>>> >>>> >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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